Infectious salmon anaemia virus (ISAV) caused a large epidemic in farmed Atlantic salmon in Chile in 2007–2009. Here, we assessed co-infection patterns of ISAV and sea lice (SL) based on surveillance data collected by the fish health authority. ISAV status and SL counts in all Atlantic salmon farms located in the 10th region of Chile were registered monthly from July 2007 through December 2009. Each farm was categorized monthly according to its ISAV and SL status. A multinomial time-space scan test using a circular window was applied to identify disease clusters, and a multivariate regression model was fitted to quantify the association between disease-clustering and farm-management factors. Most of the identified clusters (9/13) were associated with high SL burdens. There were significant associations (P < 0.05) between management factors and ISAV/SL status. Areas in which good management practices were associated with a reduced disease risk were identified. The findings of this study suggest that certain management practices can effectively reduce the risk of SL and ISAV in the face of an epidemic and will be helpful towards creating an effective disease control programme in Chile.